Read in a reference data set in Allen taxonomy format

Read in a reference data set in Allen taxonomy format

Usage

loadTaxonomy(
  taxonomyDir = getwd(),
  anndata_file = "AI_taxonomy.h5ad",
  log.file.path = getwd(),
  force = FALSE
)

Arguments

taxonomyDir

Directory containing the AIT file -OR- a direct h5ad file name -OR- a URL of a publicly accessible AIT file.

anndata_file

If taxonomyDir is a directory, anndata_file must be the file name of the anndata object (.h5ad) to be loaded in that directory. If taxonomyDir is a file name or a URL, then anndata_file is ignored.

log.file.path

Path to write log file to. Defaults to current working directory.

Value

Organized reference object ready for mapping against.